[gmx-users] ACE patch for CHARMM27

Krzysztof Kuczera kkuczera at ku.edu
Sat Sep 18 00:09:42 CEST 2010

  Hi GMXers,

I am interested in simulating blocked peptides with CHARMM (and other
force fields), using gromacs-4.5, and would appreciate some help from
more experienced GROMACS users on details.

To test things out I made a stab at creating an ACE N-terminal patch - 
this exists in OPLSAA, AMBER and CHARMM, so I added this to 

[ ACE ]
[ add ]
  1     2     CY   N    CA   C
        C    12.01100    0.51
  1     2     OY   CY   N    CA
        O    15.99900   -0.51
  1     1     CAY  CY   OY   N
        CT3  12.01100  -0.27
  3     4     HY   CAY  CY   N
        HA    1.00800   0.09
[ impropers ]
  N  CY  CA HN
[ cmap ]
  CY  N  CA  C  +N

Then built the top file with:
pdb2gmx -f -inter ala5_alpha.pdb -p ala5.top -o ala5.gro -ff charmm27 
-water tip3p -nochargegrp

selecting ACE/CT2 as my terminal types

The ala5.gro geometry looks fine, but in the ala5.top file  there is no 
bond between atoms 2 and 7 (CY==OY in the patch), so the OY oxygen 
starts to drift off in EM and MD. All other bonds are generated.

Can you tell me what is wrong here? Maybe somebody has already made a
patch that works?

I attach the ala5_alpha.pdb file


Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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